Ipyrad

Introduction

The software ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies. [1]

At the moment, there is no central installation of ipyrad, however, you can easily install it yourself using Anaconda3 as described below.

Installation

To install ipyrad you first need to load a module for Anaconda3. In this example, we use Anaconda3/2020.02 which can be found in hpc-env/8.3 (if you want to use a different version/environment you can search with module av Anaconda3 or module spider Anaconda3):

[carl]$ module load hpc-env/8.3
[carl]$ module load Anaconda/2020.02

The next step is to create a new environment for ipyrad with the command:

[carl]$ conda create --name ipyrad
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##
  environment location: /user/abcd1234/.conda/envs/ipyrad

Proceed ([y]/n)?

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

The name for the environment can be freely chosen and it will be created after you have confirmed to proceed with pressing (y and)enter. You may see a warning about an outdated conda which you can safely ignore (or, if you wish, you can switch to a newer module of Anaconda3 if available).